Apparently I've already voted in this three-year-old poll, but I sure as hell don't remember who I voted for.
For me it's a toss-up between Megaguirus and GMK Ghidorah. Megaguirus is a cool concept (the queen of the monster bugs from Rodan? Awesome!) with a great design, but the execution was just downright poor. If we're harkening back to Rodan in the year 2000, don't make the flying kaiju prop not even a fraction as mobile or lifelike as those done by Tsuburaya in 1956. Meg's wings barely flapped at any given moment, and the whole "supersonic" speeding-up effect was a joke. Even when she turns her body around in midair, it's like watching a giant turntable rotating slowly. A potentially great monster with an awesome design that's ruined by poor execution.
But ultimately, I'd have to say Ghidorah in GMK was the worst representation of any kaiju in the Millennium series. It's bad enough that Toho forced him to be saddled with the role of a guardian, which doesn't fit him at all even if it does make him a foil to Godzilla in the film. But that honestly wouldn't have bothered me as much if the design and execution were up to snuff. Alas, they were not. Hard plastic heads, wings as rigid and immobile as the 1993 Rodan, and the overall appearance and posture of a chicken make this Ghidorah a failure on all levels. He was done much better in Godzilla vs. King Ghidorah, though neither of them hold a candle to how he was brought to life in the '60s.
He may not be a popular monster, but I like Orga a lot. Having a race of kaiju-sized aliens send a lone sentry to Earth in a form-fitting ship, scanning the local life forms and trying to assimilate itself with the most powerful among them, in this case Godzilla, is a very imaginative concept, and it works really well with the idea of Godzilla's cellular regenerative abilities presented in the film. I also dig Orga's design. It's something halfway between Godzilla and the Millennian alien that exits the UFO, and I don't think its more than passing resemblance to GINO is a coincidence, considering that Orga is a character attempting to take the place of Godzilla in a movie made a year after the 1998 feature. The suit may not be as mobile as it could have been, specifically the arms, but it was still pulled off rather effectively. Unlike the clunky Spacegodzilla or Destroyer suits that could barely move and merely bumped into Godzilla and produced a bunch of sparks, Orga gets into some really involved physical fighting. He and Godzilla bite, punch and tear into each other with a real sense of animosity, and showing how Orga is utilizing Godzilla's regeneration on-screen was a nice touch. Count me as an Orga fan.